+Open data
-Basic information
Entry | Database: PDB / ID: 6cda | |||||||||
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Title | Crystal structure of L34A CzrA in the Zn(II)bound state | |||||||||
Components | ArsR family transcriptional regulator | |||||||||
Keywords | TRANSCRIPTION / Transcription regulator / Zn-binding protein / DNA Binding protein / ArsR | |||||||||
Function / homology | Function and homology information DNA-binding transcription factor activity / DNA binding / identical protein binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | |||||||||
Authors | Capdevila, D.A. / Gonzalez-Gutierrez, G. / Giedroc, D.P. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2018 Title: Functional Role of Solvent Entropy and Conformational Entropy of Metal Binding in a Dynamically Driven Allosteric System. Authors: Capdevila, D.A. / Edmonds, K.A. / Campanello, G.C. / Wu, H. / Gonzalez-Gutierrez, G. / Giedroc, D.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cda.cif.gz | 53.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cda.ent.gz | 37.2 KB | Display | PDB format |
PDBx/mmJSON format | 6cda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cda_validation.pdf.gz | 858.5 KB | Display | wwPDB validaton report |
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Full document | 6cda_full_validation.pdf.gz | 858.9 KB | Display | |
Data in XML | 6cda_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 6cda_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/6cda ftp://data.pdbj.org/pub/pdb/validation_reports/cd/6cda | HTTPS FTP |
-Related structure data
Related structure data | 6cdbC 1r1uS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 11965.628 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: rzcA, CzrA, czrA, AFO97_05125, B9Z04_11610, B9Z08_13310, BJI53_13345, BN1321_350009, EP54_06885, EQ90_13065, ERS072738_01903, ERS072840_01825, HMPREF3211_00009 Production host: Escherichia coli (E. coli) / References: UniProt: O85142 |
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-Non-polymers , 5 types, 43 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.1 M bis-tris propane (pH 9) and polyethylene glycol 550 20-22% |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: May 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 2→45.85 Å / Num. obs: 6867 / % possible obs: 96.4 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rpim(I) all: 0.028 / Rrim(I) all: 0.101 / Rsym value: 0.097 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2→2.072 Å / Redundancy: 13 % / Mean I/σ(I) obs: 2.5 / CC1/2: 0.878 / Rpim(I) all: 0.304 / Rrim(I) all: 1.112 / Rsym value: 1.069 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1r1u Resolution: 2→45.848 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.58
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso max: 114.68 Å2 / Biso mean: 40.7409 Å2 / Biso min: 19.45 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→45.848 Å
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